Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A comprehensive DNA methylation atlas for noncancer human tissue types

ABSTRACT: A comprehensive DNA methylation atlas for noncancer human tissue types

PROVIDER: PRJNA976234 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

A comprehensive DNA methylation atlas for noncancer human tissue types

Project description:Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. Here we present one of the largest comprehensive and high-resolution methylation atlas based on Reduced Representative Bisulfite Sequencing (RRBS) data of 521 noncancer tissue samples spanning 29 major types of human tissues. We systematically identified fragment-level tissue-specific methylation patterns and extensively alidated the methylation signature atlas in independent methylation datasets, orthogonal epigenomic markers, and transcription regulatory elements. Based on the rich tissue methylation atlas, we develop the first supervised tissue deconvolution approach, a deep-learning-powered model, cfSort, for sensitive and accurate tissue deconvolution in cfDNA.

2023-06-15 | GSE233417 | GEO

DNA methylation atlas of normal human cell types

Project description:DNA methylation is a fundamental epigenetic mark that governs chromatin organization, cell identity, and gene expression. Here we describe a human methylome atlas, based on deep whole-genome bisulfite sequencing allowing fragment-level analysis across thousands of unique markers for 39 cell types sorted from 205 healthy tissue samples. Replicates of the same cell-type are >99.5% identical, demonstrating robustness of cell identity programs to genetic variation and environmental perturbation. Unsupervised clustering of the atlas recapitulates key elements of tissue ontogeny, and identifies methylation patterns retained since gastrulation. Loci uniquely unmethylated in an individual cell type often reside in transcriptional enhancers and contain DNA binding sites for tissue-specific transcriptional regulators. Uniquely hyper-methylated loci are rare and are enriched for CpG islands, polycomb targets, and CTCF binding sites, suggesting a novel role in shaping cell type-specific chromatin looping. The atlas provides an essential resource for interpretation of disease-associated genetic variants, and a wealth of potential tissue-specific biomarkers for use in liquid biopsies.

| EGAS00001006791 | EGA

Mouse tissue atlas

Project description:Mouse tissue atlas

| PRJEB43879 | ENA

Sheep Tissue Atlas

Project description:Sheep Tissue Atlas

| PRJEB6169 | ENA

Arabidopsis tissue atlas

Project description:Arabidopsis tissue atlas

| PRJEB32665 | ENA

Poplar tissue types 2

Project description:Poplar tissue types 2

| PRJNA126021 | ENA

Human immunochemistry data on 83 different normal cell types from 44 tissue types from the Human Protein Atlas project

Project description:This experiment consists of expression profiles for proteins in human tissues based on immunohistochemistry tissue microarrays. The tissue and cell samples came from 144 normal individuals. Normal tissues are represented by samples from three individuals each (except for endometrium, skin, soft tissue and stomach which are represented by samples from six individuals each), one core per individual. <br> The data presented here is based on The Human Protein Atlas version 13 and Ensembl version 75.37. This entry represents a top level summary of the metadata only. For more information about the immunochemistry assays and how the tissue microarrays work for the assays, please visit the Human Protein Atlas website: http://www.proteinatlas.org/about/assays+annotation#ih

2015-07-15 | E-PROT-3 | biostudies-arrayexpress

Comprehensive Atlas of the Mouse Urinary Bladder

Project description:Comprehensive Atlas of the Mouse Urinary Bladder

| PRJNA746602 | ENA

Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types

Project description:Cell atlas of the human ocular anterior segment: Tissue-specific and shared cell types

| PRJNA817894 | ENA

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

Project description:Whole-genome transcriptional profiles of rice cell types, isolated by laser-capture microdissection. The first comprehensive multi-organ cell type transcriptome atlas from a plant, with 40 distinct cell types from several developmental stages of seeds, shoots and roots, reveals cell-specific promoter motifs, interaction partner candidates, hormone response centers, and other previously unrecognized cellular properties and patterns. Keywords: Cell type comparison

2008-10-16 | GSE13161 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data